Contacts of the helix formed by residues 662 - 673 (chain A) in PDB entry 1Q3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 662 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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609A ALA 3.9 11.2 - - - -
627A LEU* 5.7 0.4 - - - -
628A GLN* 3.4 0.9 - - - -
660A LYS 4.0 1.2 + - - -
661A VAL* 1.3 77.9 - - - +
663A HIS* 1.3 66.6 + - - -
664A ARG 3.3 2.5 - - - -
665A GLN* 3.0 9.1 + - - +
666A VAL* 3.0 22.1 + - - +
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Residues in contact with HIS 663 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LEU* 2.7 35.6 - - + +
608A GLY 3.7 0.2 + - - -
609A ALA* 3.2 23.0 + - - +
628A GLN* 2.8 39.9 + - - +
662A GLY* 1.3 70.4 - - - +
664A ARG* 1.3 59.5 + - - +
666A VAL* 3.2 1.9 + - - +
667A VAL* 2.9 48.7 + - + +
2C ALA* 3.0 34.9 + - + +
3C GLN 3.7 1.2 - - - -
4C THR* 2.5 27.5 + - - -
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Residues in contact with ARG 664 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609A ALA 5.1 0.2 + - - -
662A GLY 3.3 1.0 - - - -
663A HIS* 1.3 82.5 - - + +
665A GLN* 1.3 59.7 + - - +
667A VAL* 3.6 7.5 - - - +
668A ASN* 3.0 38.2 + - + +
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Residues in contact with GLN 665 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A VAL* 3.4 25.6 - - + -
662A GLY* 3.0 7.8 + - - +
664A ARG* 1.3 81.0 - - + +
666A VAL* 1.3 57.7 + - - +
668A ASN* 3.4 18.5 + - - +
669A MET* 2.9 36.2 + - - +
672A GLN* 4.5 2.6 - - - +
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Residues in contact with VAL 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606A LEU* 4.0 18.8 - - + -
628A GLN* 3.6 24.5 - - + -
650A LEU* 4.3 5.2 - - + -
653A VAL* 4.2 17.7 - - + -
658A VAL* 4.0 11.7 - - + -
661A VAL* 3.4 25.1 - - + -
662A GLY 3.0 13.7 + - - +
663A HIS 3.7 5.8 - - - +
665A GLN* 1.3 72.5 - - - +
667A VAL* 1.3 68.6 + - - +
669A MET* 3.0 10.4 + - - +
670A ILE* 3.0 30.7 + - + +
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Residues in contact with VAL 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A LEU* 4.1 8.3 - - + -
663A HIS* 2.9 57.8 + - + +
664A ARG* 3.6 7.2 - - - +
666A VAL* 1.3 76.1 - - - +
668A ASN* 1.3 56.7 + - - +
670A ILE* 3.1 12.5 + - - +
671A ARG* 2.9 57.0 + - - +
4C THR* 4.0 20.2 - - + +
6C LEU* 4.3 7.1 - - + +
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Residues in contact with ASN 668 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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664A ARG* 3.0 29.3 + - + +
665A GLN* 3.4 18.0 + - - +
667A VAL* 1.3 79.2 - - - +
669A MET* 1.3 57.6 + - - +
671A ARG* 3.1 13.2 + - - +
672A GLN* 2.8 44.1 + - - +
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Residues in contact with MET 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653A VAL* 4.1 13.7 - - + +
654A ASN* 3.8 8.6 - - + +
656A GLN* 3.2 46.2 - - + +
657A ASN 5.4 0.7 - - - +
658A VAL* 3.8 24.5 - - + -
661A VAL* 4.7 4.3 - - - -
665A GLN* 2.9 40.0 + - - +
666A VAL* 3.0 10.3 + - - +
668A ASN* 1.3 74.8 - - - +
670A ILE* 1.3 63.4 + - - +
672A GLN* 3.2 34.9 + - - +
673A GLY 3.4 5.4 + - - -
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Residues in contact with ILE 670 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A PHE* 4.1 18.7 - - + -
604A PHE* 4.3 11.4 - - + -
606A LEU* 4.1 10.8 - - + -
650A LEU* 4.3 9.9 - - + -
653A VAL* 3.9 20.2 - - + -
654A ASN* 4.9 2.4 - - - +
666A VAL* 3.0 31.6 + - + +
667A VAL 3.1 6.3 + - - +
669A MET* 1.3 72.1 - - - +
671A ARG* 1.3 68.6 + - - +
673A GLY* 3.3 11.3 + - - -
674A GLY 4.0 5.7 + - - +
676A THR 4.8 2.1 - - - +
677A LEU* 3.9 26.3 - - + +
6C LEU* 3.5 33.9 - - + -
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Residues in contact with ARG 671 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667A VAL* 2.9 38.5 + - + +
668A ASN* 3.2 16.9 - - - +
670A ILE* 1.3 78.1 - - - +
672A GLN* 1.3 64.8 + - - +
674A GLY* 2.9 19.3 + - - +
4C THR* 4.3 8.5 - - - +
5C ARG 4.6 2.8 + - - -
6C LEU* 3.7 25.1 - - + +
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Residues in contact with GLN 672 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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665A GLN* 4.5 1.9 - - - +
668A ASN* 2.8 45.5 + - - +
669A MET* 3.2 31.0 + - - +
671A ARG* 1.3 77.0 - - - +
673A GLY* 1.3 58.1 + - - +
674A GLY* 3.0 5.9 + - - -
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Residues in contact with GLY 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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654A ASN* 4.0 12.7 + - - -
669A MET 3.4 4.0 + - - -
670A ILE 3.3 7.3 + - - -
671A ARG 3.0 1.8 + - - -
672A GLN* 1.3 76.2 - - - +
674A GLY* 1.3 61.8 - - - +
675A ASN 3.3 3.6 + - - -
676A THR* 3.4 31.5 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il